Skip to main content

The NCI Community Hub (NCI Hub) will be offline for maintenance December 2-3, 2022 as we migrate URLs from NCIhub.org to NCIhub.cancer.gov. The current address will automatically redirect to the new URL. The NCI Hub will continue to function as usual after the migration. Please be sure to update any bookmarks or favorites to the new URL. close

Next-Generation Clustered Heat Maps (NG-­CHM)

By Weinstein John1, Bradley Broom1

1. MD Anderson Cancer Center

You must login to access the full resource.

Published on

Abstract

Clustered Heat Maps (CHMs) have been referred to as the ubiquitous visual icons of post-genomic biology -- the most frequent type of visualization for large molecular profiling databases. However, “traditional” CHMs are static images -- a serious limitation. Accordingly, we have now developed an interactive CHM-based environment for deep exploration of patterns in omic data – “Next-Generation” CHMs (NG-CHMs) in which one can zoom and navigate as in a Google map, link out to a variety of external information sources, invoke a statistical toolbox, change color schemes on the fly, save all metadata needed to reproduce the map months or years later, and produce high-resolution, publication-ready images. We propose to mature and harden that development (Aim #1), adding more toolbox features, increasing user- friendliness, increasing shearability, fleshing out an NG-CHM builder with 4 levels of sophistication for different degrees of expertise (Aim #2), and refining the visualizations to fit the needs of non-specialist cancer biologists and clinical researchers. We have also formed working relationships for linking NG- CHMs with other strong bioinformatics resources (Aim #3), including cBio, the UCSC Genome Browser and Cancer Genome Browser, Regulome Explorer, and TCPA and TANRIC, as well as “home-grown” developments like SpliceSeq and Mbatch. Analogous linkage can be developed with other ITCR software. We also propose to develop additional NG-CHM compendia for TCGA and ICGC (Aim #4) and to interact extensively with the cancer and bioinformatics communities by providing training through a combination of comprehensive written documentation, tutorial videos, webinars, workshops, and formats for obtaining feedback (Aim #5).

Submitter

Mervi Heiskanen

National Cancer Institute

Tags